Discretization error cancellation in the plane-wave approximation of periodic Hamiltonians with Coulomb singularities

In solid-state physics, energies of molecular systems are usually computed with a plane-wave discretization of Kohn-Sham equations. A priori estimates of plane-wave convergence for periodic Kohn-Sham calculations with pseudopotentials have been proved , however in most computations in practice, plane-wave cut-offs are not tight enough to target the desired accuracy. It is often advocated that the real quantity of interest is not the value of the energy but of energy differences for different configurations. The computed energy difference is believed to be much more accurate because of `discretization error cancellation', since the sources of numerical errors are essentially the same for different configurations. For periodic linear Hamiltonians with Coulomb potentials, error cancellation can be explained by the universality of the Kato cusp condition. Using weighted Sobolev spaces, Taylor-type expansions of the eigenfunctions are available yielding a precise characterization of this singularity. This then gives an explicit formula of the first order term of the decay of the Fourier coefficients of the eigenfunctions. It enables one to prove that errors on eigenvalue differences are reduced but converge at the same rate as the error on the eigenvalue.Comment: 14 pages, 3 figures, improved result on main theorem, corrected typo

Sensitivity of Ru(bpy)_2dppz^(2+) Luminescence to DNA Defects

The luminescent characteristics of Ru(bpy)_2dppz^(2+) (dppz = dipyrido[3,2-a:2′,3′-c]phenazine), a DNA light switch, were investigated in the presence of oligonucleotides containing single base mismatches or an abasic site. In water, the ruthenium luminescence is quenched, but, bound to well matched duplex DNA, the Ru complex luminesces. Here we show that with DNAs containing a defect, rac-, Δ-, and Λ-Ru(bpy)_2dppz^(2+) exhibit significant luminescent enhancements above that with well matched DNA. In the presence of a single base mismatch, large luminescent enhancements are evident for the Δ-Ru isomer; the Λ-isomer shows particularly high luminescence bound to an oligonucleotide containing an abasic site. Similar increases are not evident with two common DNA-binding organic fluorophores, ethidium bromide and TO-PRO-3. Titrations with hairpin oligonucleotides containing a variable mismatch site show correlation between the level of luminescent enhancement and the thermodynamic destabilization associated with the mismatch. This correlation is reminiscent of that found earlier for a bulky rhodium complex that binds mismatched DNA sites through metalloinsertion, where the complex binds the DNA from the minor groove side, ejecting the mismatched bases into the major groove. Differential quenching studies with minor and major groove quenchers and time-resolved emission studies support this metalloinsertion mode for the dppz complex at the defect site. Certainly these data underscore the utility of Ru(bpy)_2dppz^(2+) as a sensitive luminescent reporter of DNA and its defects

Putative cell adhesion membrane protein Vstm5 regulates neuronal morphology and migration in the central nervous system

During brain development, dynamic changes in neuronal membranes perform critical roles in neuronal morphogenesis and migration to create functional neural circuits. Among the proteins that induce membrane dynamics, cell adhesion molecules are important in neuronal membrane plasticity. Here, we report that V-set and transmembrane domain-containing protein 5 (Vstm5), a cell-adhesion-like molecule belonging to the Ig superfamily, was found in mouse brain. Knock-down of Vstm5 in cultured hippocampal neurons markedly reduced the complexity of dendritic structures, as well as the number of dendritic filopodia. Vstm5 also regulates neuronal morphology by promoting dendritic protrusions that later develop into dendritic spines. Using electroporationin utero, we found that Vstm5 overexpression delayed neuronal migration and induced multiple branches in leading processes during corticogenesis. These results indicate that Vstm5 is a new cell-adhesion-like molecule and is critically involved in synaptogenesis and corticogenesis by promoting neuronal membrane dynamics.SIGNIFICANCE STATEMENTNeuronal migration and morphogenesis play critical roles in brain development and function. In this study, we demonstrate for the first time that V-set and transmembrane domain-containing protein 5 (Vstm5), a putative cell adhesion membrane protein, modulates both the position and complexity of central neurons by altering their membrane morphology and dynamics. Vstm5 is also one of the target genes responsible for variations in patient responses to treatments for major depressive disorder. Our results provide the first evidence that Vstm5 is a novel factor involved in the modulation of the neuronal membrane and a critical element in normal neural circuit formation during mammalian brain development.</jats:p

Genome-wide analysis to predict protein sequence variations that change phosphorylation sites or their corresponding kinases

We define phosphovariants as genetic variations that change phosphorylation sites or their interacting kinases. Considering the essential role of phosphorylation in protein functions, it is highly likely that phosphovariants change protein functions and may constitute a proportion of the mechanisms by which genetic variations cause individual differences or diseases. We categorized phosphovariants into three subtypes and developed a system that predicts them. Our method can be used to screen important polymorphisms and help to identify the mechanisms of genetic diseases

Joseon mummies before mummy studies began in Korea

Mummy studies in Korea are instrumental in reconstructing the health and disease status of pre-modern Joseon peoples using firm scientific evidence. However, this scientific approach to such investigations in Korea is a relatively new discipline which began only within the last decade. Previous studies on Joseon tombs and their contents were performed exclusively by dress historians because most of the artefacts recoverable from Joseon tombs were textiles. In this report, we examine some of the excavation records left by dress historians in order to elucidate the approximate number and preservation status of Korean mummies discovered prior to the advent of their scientific investigation

Integrated Information System for Sustainable Urban Regeneration

Information systems are widely used in urban planning process for communication between different side actors. However, most of them have been implemented without providing possibilities for decision makers to participate together with urban planners in the process. This research aims to outline a framework where an interactive model for decision making plays a key role in creating a collaborative environment. The proposal regards the information representation as the main instrument for encouraging a constructive dialog between different actors. The focus is on the relationship between three elements of information representation: level of detail, type of visualization and interaction. Combining these elements, information can be provided in a dynamic way enabling more effective exploration and understanding. The proposed strategy implements a digital model that operates on different scales and levels in order to support the key stages of the planning process for sustainable urban regeneration in Bulgaria. Positional approach is used to define the functionality and decision making operation for the selected process. As a result research ideas about the use of the digital model are presented

Potassium chloride elicits enhancement of bilobalide and Ginkgolides production by Ginkgo biloba cell cultures

This study investigated the ability of potassium chloride (KCl) to elicit the production of bilobalide (BB), ginkgolide A (GA) and ginkgolide B (GB) by Ginkgo biloba cell suspension cultures. The salt stress by KCl treatments increased production of BB, GA and GB in both suspended cells and cultured medium. Especially, treatment of KCl 800 mM of highest concentration was stimulated emission into cultured medium BB, GA and GB compounds accumulated in cells. Although KCl 800 mM severely inhibited cells growth, the maximum content of GA and GB in cells was obtained in the treatment of KCl 800 mM, which was 1.9 and 4.0 times higher than the control. These results thus suggest that salt stress can afford enhanced production of secondary metabolites by plant cell cultures

Intra-day variability observations and the VLBI structure analysis of quasar S4 0917+624

The IDV observations of S4 0917+624 were carried out monthly, from August 2005 to January 2010, with the Urumqi 25m radio telescope at 4.8 GHz. The quasar S4 0917+624 exhibits only very weak or no IDV during our 4.5 year observing interval. Prior to the year 2000, the source S4 0917+624 was one of the most prominent IDV sources. Our new data indicate that the previous strong IDV has ceased. We analyzed the long-term VLBI structural variability using Gaussian model-fitting. From this we obtained the flux densities and the deconvolved sizes of core and inner-jet components of the source. We studied the properties such as core fraction, angular size, spectral index, and brightness temperature of VLBI core for S4 0917+624, as well as the time delay between 5 and 15 GHz variations, and compared them with the IDV properties of S4 0917+624. The source shows ejection of several jet components that are suspected to have partially reduced the IDV amplitude of S4 0917+624. However, during 2005-2006, the VLBI core size was comparable to the size before the year 2000, but no strong IDV was detected in the period, suggesting that the quenching effect due to source size changes may not be responsible for the lack of strong IDV after the year 2000. The refractive scattering properties for the strong IDV phase of S4 0917+624 before the year 2000 are discussed. The disappearance of strong IDV in S4 0917+624 after the year 2000 is a mystery and cannot be explained via the quenching effect by changes in the observable VLBI structure. However, it may be caused by changes in the interstellar medium, i.e. by interstellar weather, which induces changes in the scintillation pattern on timescales of several years. Further coordinated multi-frequency observations will be required to distinguish between the effect of source-intrinsic variability and changing properties of the interstellar medium.Comment: 8 pages, 6 figures, accepted for publication in A&